In 1643, the English Parliament called upon "learned, godly and judicious Divines", to meet at Westminster Abbey in order to provide advice on issues of worship, doctrine, government and discipline of the Church of England. Their meetings, over a period of five years, produced the confession of faith, as well as a Larger Catechism and a Shorter Catechism. For more than three centuries, various churches around the world have adopted the confession and the catechisms as their standards of doctrine, subordinate to the Bible.

The Westminster Confession of Faith was modified and adopted by Congregationalists in England in the form of the Savoy Declaration (1658). Likewise, the Baptists of England modified the Savoy Declaration to produce the Second London Baptist Confession (1689). English Presbyterians, Congregationalists, and Baptists would together (with others) come to be known as Nonconformists, because they did not conform to the Act of Uniformity (1662) establishing the Church of England as the only legally-approved church, though they were in many ways united by their common confessions, built on the Westminster Confession.

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During the English Civil War (1642-1649), the English Parliament raised armies in an alliance with the Covenanters who by then were the de facto government of Scotland, against the forces of the king, Charles I of England. The purpose of the Westminster Assembly, in which 121 Puritan clergymen participated, was to provide official documents for the reformation of the Church of England. The Church of Scotland had recently overthrown its bishops and adopted presbyterianism (see Bishops' Wars). For this reason, as a condition for entering into the alliance with England, the Scottish Parliament formed the Solemn League and Covenant with the English Parliament, which meant that the Church of England would abandon episcopalianism and consistently adhere to Calvinistic standards of doctrine and worship. The Confession and Catechisms were produced in order to secure the help of the Scots against the king.

The Scottish Commissioners who were present at the Assembly were satisfied with the Confession of Faith, and in 1646, the document was sent to the English parliament to be ratified, and submitted to the General Assembly of the Scottish Kirk. The Church of Scotland adopted the document, without amendment, in 1647. In England, the House of Commons returned the document to the Assembly with the requirement to compile a list of proof texts from Scripture. After vigorous debate, the Confession was then in part adopted as the Articles of Christian Religion in 1648, by act of the English parliament, omitting some sections and chapters. The next year, the Scottish parliament ratified the Confession without amendment.

In 1660, the restoration of the British monarchy and of the Anglican episcopacy resulted in the nullification of these acts of the two parliaments. However, when William of Orange replaced the Roman Catholic King James II of England, he gave royal sanction to Scottish parliament's ratification of the Confession, again without change, in 1690.

Even more controversially, it states that the Pope is the Antichrist, that the Roman Catholic mass is a form of idolatry, and rules out marriage with non-Christians. These formulations were repudiated by the various bodies which adopted the confession (for instance, the Church of Scotland, though its ministers are still free to adhere to the full confession and some do), but the confession remains part of the official doctrine of some other Presbyterian churches. For example, the Presbyterian Church of Australia holds to the Westminster Confession of Faith as its standard, subordinate to the Word of God, and read in the light of a declaratory statement.[1]

The first American Presbyterian ministers were New England Congregationalists, whose congregations originated with the migration from England to the Dutch colony in America as early as the 1640s, and Presbyterian immigrants from Scotland, Ireland and Wales. The first American presbytery, uniting some of these independent congregations and those of the British immigrants, was formed in 1706. This body grew large enough to form the first synod in Philadelphia in 1716. Prior to 1729, some presbyteries required candidates for the ministry to profess adherence to the Westminster Confession. When the Synod of Philadelphia met in 1729 to adopt the Westminster Confession as the doctrinal standard, it required all ministers to declare their approval of the Westminster Confession of Faith and catechisms. At the same time, the Adopting Act allowed candidates and ministers to scruple articles within the Confession. Whether or not the article scrupled was essential or nonessential was judged by the presbytery with jurisdiction over the candidate's examination. This allowance implied a difference, within the standards themselves, between things that are essential and necessary to the Christian faith, and things that are not. This compromise left a permanent legacy to following generations of Presbyterians in America, to decide what is meant by "essential and necessary", resulting in permanent controversies over the manner in which a minister is bound to accept the document; and it has left the American versions of the Westminster Confession more amenable to the will of the church to amend it.

The American revision of 1787–1789 removes from the Confession and the Catechisms mention of certain duties of the civil government in relationship to the church, reflecting the American tendency to reject a relationship between the church and state. It also removes explicit identification of the Pope as the Antichrist.

In 1910, the PCUSA attempted to specify that a supernatural perspective is necessary and essential, according to the Bible and the Westminster standards. This perspective was articulated in terms of five doctrinal issues:

Similar movements in the southern PCUS away from strict interpretations of the Westminster Confession, culminating in its eventual merger into the PCUSA in 1983, led to the creation of the Presbyterian Church in America in 1973. The PCA holds the 1789 American revision of the Westminster Confession as its standard "with two minor exceptions, namely, the deletion of strictures against marrying one's wife's kindred (XXIV,4), and the reference to the Pope as the antichrist (XXV,6)."[1]. In general, the PCA allows greater leeway than the OPC for elders to take personal exception to some articles in the Confession.